Mercurial > repos > recetox > waveica

annotate waveica.xml @ 2:d08deef1eb44 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit e33ef984e78721ed37d825c6672795a539a461e1"
author recetox
date Fri, 12 Nov 2021 09:14:04 +0000
parents 2bcfd5b450bb
children e3726251a055
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d08deef1eb44 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit e33ef984e78721ed37d825c6672795a539a461e1"
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1 <tool id="waveica" name="WaveICA" version="0.1.0+galaxy2" python_template_version="3.5">
0
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2
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3 <description>removal of batch effects for untargeted metabolomics data</description>
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4
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5 <requirements>
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6 <container type="docker">recetox/waveica:0.1.0-recetox0</container>
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7 </requirements>
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8
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9 <command detect_errors="aggressive"><![CDATA[
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10 Rscript
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11 -e 'source("${__tool_directory__}/waveica_wrapper.R")'
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12
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13 -e 'normalized_data <- waveica(
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14 data = "$data",
2
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15 wavelet_filter = "$wf.wavelet_filter",
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16 wavelet_length = "$wf.wavelet_length",
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17 k = $k,
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18 t = $t,
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19 t2 = $t2,
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20 alpha = $alpha,
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21 exclude_blanks = $exclude_blanks
0
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22 )'
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23
2
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24 -e 'store_data(normalized_data,"$normalized_data")'
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25 ]]></command>
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26
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27 <inputs>
2
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28 <param type="data" name="data" label="Feature table" format="csv" help=""/>
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29 <conditional name="wf">
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30 <param type="select" name="wavelet_filter" label="Wavelet transform filter" help="wavelet function and filter length [1] (see footnotes for more details)">
d08deef1eb44 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit e33ef984e78721ed37d825c6672795a539a461e1"
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31 <option value="d" selected="True">Daubechies</option>
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32 <option value="la" >Least Asymetric</option>
d08deef1eb44 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit e33ef984e78721ed37d825c6672795a539a461e1"
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33 <option value="bl" >Best Localized</option>
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34 <option value="c" >Coiflet</option>
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35 </param>
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36 <when value="d">
d08deef1eb44 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit e33ef984e78721ed37d825c6672795a539a461e1"
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37 <param name="wavelet_length" type="select" label="filter length">
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38 <option value="2" selected="True">2</option>
d08deef1eb44 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit e33ef984e78721ed37d825c6672795a539a461e1"
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39 <option value="4">4</option>
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40 <option value="6">6</option>
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41 <option value="8">8</option>
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42 <option value="10">10</option>
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43 <option value="12">12</option>
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44 <option value="14">14</option>
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45 <option value="16">16</option>
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46 <option value="18">18</option>
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47 <option value="20">20</option>
0
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48 </param>
2
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49 </when>
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50 <when value="la">
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51 <param name="wavelet_length" type="select" label="filter length">
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52 <option value="8">8</option>
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53 <option value="10">10</option>
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54 <option value="12">12</option>
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55 <option value="14">14</option>
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56 <option value="16">16</option>
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57 <option value="18">18</option>
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58 <option value="20">20</option>
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59 </param>
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60 </when>
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61 <when value="bl">
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62 <param name="wavelet_length" type="select" label="filter length">
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63 <option value="14">14</option>
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64 <option value="18">18</option>
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65 <option value="20">20</option>
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66 </param>
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67 </when>
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68 <when value="c">
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69 <param name="wavelet_length" type="select" label="filter length">
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70 <option value="6">6</option>
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71 <option value="12">12</option>
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72 <option value="18">18</option>
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73 <option value="24">24</option>
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74 <option value="30">30</option>
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75 </param>
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76 </when>
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77 </conditional>
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78 <param type="integer" value="20" name="k" label="Number of components to decompose" help="maximal component that ICA decomposes"/>
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79 <param type="float" value="0.05" name="t" label="Batch-association threshold" help="threshold to consider a component associate with the batch,
0
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80 should be between 0 and 1"/>
2
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81 <param type="float" value="0.05" name="t2" label="Group-association threshold" help="threshold to consider a component associate with the group,
0
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82 should be between 0 and 1"/>
2
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83 <param type="float" value="0" name="alpha" label="Alpha" help="trade-off value between the independence of samples (temporal ICA) and variables (spatial ICA), should be between 0 and 1"/>
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84 <param name="exclude_blanks" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Remove blanks" help="Excludes blank samples from the output" />
0
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85 </inputs>
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86
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87 <outputs>
2
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88 <data name="normalized_data" format="tsv" />
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89 </outputs>
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90
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91 <tests>
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92 <test>
2
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93 <param name="data" value="input_data.csv" ftype="csv" />
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94 <param name="wavelet_filter" value="d" />
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95 <param name="filter_length" value="2" />
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96 <param name="k" value="20" />
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97 <param name="t" value="0.05" />
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98 <param name="t2" value="0.05" />
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99 <param name="alpha" value="0" />
2
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100 <output name="normalized_data" file="normalized_data.tsv" />
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101 </test>
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102 <test expect_failure="true">
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103 <param name="data" value="na_data.csv" ftype="csv" />
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104 </test>
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105 <test expect_failure="true">
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106 <param name="data" value="incomplete_metadata_data.csv" ftype="csv" />
0
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107 </test>
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108 </tests>
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109
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110 <help><![CDATA[
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111 **Description**
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112
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113 Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis. The WaveICA R package provides a new algorithm to removing batch effects for metabolomics data.
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114
2
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115 The input is an intensity-by-feature table with metadata in the following format:
0
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116
2
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117 +---------------+--------+------------+----------------+-------+------------+--------------+-------------+-------------+-----+
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118 | sampleName | class | sampleType | injectionOrder | batch | M85T34 | M86T41 | M86T518 | M86T539 | ... |
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119 +===============+========+============+================+=======+============+==============+=============+=============+=====+
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120 | VT_160120_002 | sample | sample | 1 | 1 | 228520.064 | 35646729.215 | 2386896.979 | 1026645.836 | ... |
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121 +---------------+--------+------------+----------------+-------+------------+--------------+-------------+-------------+-----+
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122 | QC1 | sample | QC | 2 | 1 | 90217.384 | 35735702.457 | 2456290.696 | 1089246.460 | ... |
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123 +---------------+--------+------------+----------------+-------+------------+--------------+-------------+-------------+-----+
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124 | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
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125 +---------------+--------+------------+----------------+-------+------------+--------------+-------------+-------------+-----+
0
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126
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127
2
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128 + the input table must not contain missing values. Missing intensities must be filled with 0.
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129 + **sampleType** column accepts three possible values: [QC, sample, blank] (case insensitive).
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130 + **class** column is used to denote a biological group of a sample (e.g., positive/negative species). The column accepts any values.
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131 + the **output** is the same table with corrected feature intensities.
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132
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133 .. rubric:: **Footnotes**
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134 .. [1] for details on wavelet filter parameters refer to R `wavelets::wt.filter <https://www.rdocumentation.org/packages/wavelets/versions/0.3-0.2/topics/wt.filter>`_;
0
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135
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136 ]]></help>
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137
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138 <citations>
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139 <citation type="doi">10.1016/j.aca.2019.02.010</citation>
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140 </citations>
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141
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142 </tool>